Re: Extraction of force data

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Mar 22 2007 - 22:29:20 CDT

awk is a scripting language used in linux. The problem is that tcl
has no knowledge of awk.

What OS are you using? Ideally, you would run that from the command
line, but actually like this, I think would be simpler:

awk '{if ($1=="SMD) print $0}' ubq_ww_pcv.log > analysis/smd.dat

But if you're using windows, you'd have to use something like Cygwin
to run that command.

On Mar 22, 2007, at 10:12 PM, Viral D. Tejani wrote:

> Hi,
>
> I am not too experienced w/ NAMD, and am practicing force
> extraction using the NAMD Tutorial. From the TkConsole, I used the
> following command and am getting the following results. (I copied
> and pasted the exact text from the TkConsole)
>
> >Main< (Tutorial) 4 % dir
> .:
> ubq.pdb ubq.psf ubq_wb.pdb ubq_wb.psf ubq_ws.pdb
> ubq_ws.psf ubq_ww_eq.pdb ubq_ww_eq.ref ubq_ww_eq2.ref ubq_ww_pcv.dcd
> ubq_ww_pcv.log
> >Main< (Tutorial) 5 % cat ubq_ww_pcv.log | awk {if ($1=="SMD")
> print $0}'> analysis/smd.dat
> can't read "1": no such variable
> >Main< (Tutorial) 6 %
>
>
> I am using the same output files as provided by the NAMD website,
> and do not know why this error is being generated and how to
> correct it. Any assistance is appreciated.
>
> - Viral

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